Plots

knitr::opts_chunk$set(echo = TRUE)

library(tidyverse)

## ── Attaching packages ─────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──

## ✓ ggplot2 3.2.1     ✓ purrr   0.3.3
## ✓ tibble  2.1.3     ✓ dplyr   1.0.2
## ✓ tidyr   1.0.2     ✓ stringr 1.4.0
## ✓ readr   1.3.1     ✓ forcats 0.4.0

## ── Conflicts ────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()

library(here)

## here() starts at /Users/ericmarty/Repositories/COVID-stochastic-fitting

path <- "../output/current/"

allfiles <- list.files(path, ".csv")

for(f in allfiles) {
  fname <- paste0(path,f)
dat <- read.csv(fname) %>%
  filter(variable %in% c("actual_daily_cases")) %>%
  mutate(date = as.Date(date))

read.csv(fname) %>%
  filter(variable %in% c("daily_cases")) %>%
  filter(sim_type == "status_quo") %>%
  mutate(date = as.Date(date)) %>%
  filter(date <= (Sys.Date() + 7*4)) %>%
  ggplot(aes(x = date, y = median_value)) +
  geom_ribbon(aes(ymin = lower_80, ymax = upper_80), alpha = 0.2) +
  geom_line() +
  geom_line(data = dat, aes(x = date, y = mean_value), color = "blue") +
  ylab("daily cases") +
  ggtitle(f) -> out
print(out)

dat <- read.csv(fname) %>%
  filter(variable %in% c("actual_daily_deaths")) %>%
  mutate(date = as.Date(date))
read.csv(fname) %>%
  filter(variable %in% c("daily_deaths")) %>%
  filter(sim_type == "status_quo") %>%
  mutate(date = as.Date(date)) %>%
  filter(date <= (Sys.Date() + 7*4)) %>%
  ggplot(aes(x = date, y = median_value)) +
  geom_ribbon(aes(ymin = lower_80, ymax = upper_80), alpha = 0.2) +
  geom_line() +
  ylab("daily deaths") +
  geom_line(data = dat, aes(x = date, y = mean_value), color = "blue") +
  ggtitle(f) -> out3
print(out3)

read.csv(fname) %>%
  filter(variable %in% c("combined_trend", "latent_trend", "mobility_trend")) %>%
  filter(sim_type == "status_quo") %>%
  mutate(date = as.Date(date)) %>%
  ggplot(aes(x = date, y = mean_value)) +
  geom_point(aes(color = variable)) +
  ggtitle(f) -> out2
print(out2)
}

## Warning: Removed 9 rows containing missing values (geom_path).

## Warning: Removed 1 rows containing missing values (geom_path).

## Warning: Removed 10 rows containing missing values (geom_path).

## Warning: Removed 17 rows containing missing values (geom_path).

## Warning: Removed 9 rows containing missing values (geom_path).

## Warning: Removed 10 rows containing missing values (geom_path).

## Warning: Removed 13 rows containing missing values (geom_path).

## Warning: Removed 3 rows containing missing values (geom_path).

## Warning: Removed 8 rows containing missing values (geom_path).

## Warning: Removed 10 rows containing missing values (geom_path).

## Warning: Removed 26 rows containing missing values (geom_path).

## Warning: Removed 16 rows containing missing values (geom_path).

## Warning: Removed 14 rows containing missing values (geom_path).

## Warning: Removed 9 rows containing missing values (geom_path).

## Warning: Removed 20 rows containing missing values (geom_path).

## Warning: Removed 9 rows containing missing values (geom_path).

## Warning: Removed 9 rows containing missing values (geom_path).

## Warning: Removed 9 rows containing missing values (geom_path).

## Warning: Removed 21 rows containing missing values (geom_path).

## Warning: Removed 14 rows containing missing values (geom_path).

## Warning: Removed 57 rows containing missing values (geom_path).

## Warning: Removed 17 rows containing missing values (geom_path).

## Warning: Removed 16 rows containing missing values (geom_path).

## Warning: Removed 14 rows containing missing values (geom_path).

## Warning: Removed 8 rows containing missing values (geom_path).

## Warning: Removed 22 rows containing missing values (geom_path).

## Warning: Removed 15 rows containing missing values (geom_path).

## Warning: Removed 1 rows containing missing values (geom_path).

## Warning: Removed 21 rows containing missing values (geom_path).

## Warning: Removed 1 rows containing missing values (geom_path).

## Warning: Removed 20 rows containing missing values (geom_path).

## Warning: Removed 12 rows containing missing values (geom_path).

## Warning: Removed 13 rows containing missing values (geom_path).

## Warning: Removed 7 rows containing missing values (geom_path).

## Warning: Removed 16 rows containing missing values (geom_path).

## Warning: Removed 13 rows containing missing values (geom_path).

## Warning: Removed 15 rows containing missing values (geom_path).

## Warning: Removed 13 rows containing missing values (geom_path).

## Warning: Removed 29 rows containing missing values (geom_path).

## Warning: Removed 13 rows containing missing values (geom_path).

## Warning: Removed 12 rows containing missing values (geom_path).

## Warning: Removed 19 rows containing missing values (geom_path).

## Warning: Removed 14 rows containing missing values (geom_path).

## Warning: Removed 9 rows containing missing values (geom_path).

## Warning: Removed 15 rows containing missing values (geom_path).

## Warning: Removed 18 rows containing missing values (geom_path).

## Warning: Removed 36 rows containing missing values (geom_path).

## Warning: Removed 10 rows containing missing values (geom_path).

## Warning: Removed 17 rows containing missing values (geom_path).

## Warning: Removed 21 rows containing missing values (geom_path).